{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test tutorial\n",
    "\n",
    "This isn't really intended to be a useful tutorial, it's there to allow us to excercise the automated testing code.\n",
    "\n",
    "@TAGS: #testing #basics "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "IPythonConsole.ipython_useSVG=True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sun Oct 16 09:33:19 2016\n"
     ]
    }
   ],
   "source": [
    "import time\n",
    "print(time.asctime()) # doctest: IGNORE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Oc1ccccc1'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.CanonSmiles(\"c1ccccc1O\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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      "image/svg+xml": [
       "<?xml version='1.0' encoding='iso-8859-1'?>\n",
       "<svg version='1.1' baseProfile='full'\n",
       "              xmlns:svg='http://www.w3.org/2000/svg'\n",
       "                      xmlns:rdkit='http://www.rdkit.org/xml'\n",
       "                      xmlns:xlink='http://www.w3.org/1999/xlink'\n",
       "                  xml:space='preserve'\n",
       "width='450px' height='150px' >\n",
       "<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='450' height='150' x='0' y='0'> </rect>\n",
       "<path d='M 201.372,143.182 122.642,143.182' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 189.562,127.436 134.452,127.436' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 201.372,143.182 240.736,75' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 122.642,143.182 83.2773,75' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 83.2773,75 122.642,6.81818' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 102.818,72.6457 130.374,24.9184' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 122.642,6.81818 201.372,6.81818' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 201.372,6.81818 240.736,75' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 193.64,24.9184 221.195,72.6457' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 240.736,75 273.349,75' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 273.349,75 305.961,75' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<text x='305.961' y='82.5' style='font-size:14px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>OH</tspan></text>\n",
       "</svg>\n"
      ],
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fd494ab0f30>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.MolFromSmiles('c1ccccc1O')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "hello\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'CNc1ccccc1'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(\"hello\")\n",
    "# comment\n",
    "Chem.CanonSmiles(\"c1ccccc1NC\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "Some nice explanatory text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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      "image/svg+xml": [
       "<?xml version='1.0' encoding='iso-8859-1'?>\n",
       "<svg version='1.1' baseProfile='full'\n",
       "              xmlns:svg='http://www.w3.org/2000/svg'\n",
       "                      xmlns:rdkit='http://www.rdkit.org/xml'\n",
       "                      xmlns:xlink='http://www.w3.org/1999/xlink'\n",
       "                  xml:space='preserve'\n",
       "width='450px' height='150px' >\n",
       "<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='450' height='150' x='0' y='0'> </rect>\n",
       "<path d='M 312.382,19.4188 257.052,42.9632' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 257.052,42.9632 236.527,27.5251' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 236.527,27.5251 216.002,12.0869' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 201.992,9.79891 180.832,18.803' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 180.832,18.803 159.672,27.8072' style='fill:none;fill-rule:evenodd;stroke:#7F7F7F;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 222.02,113.116 274.095,83.0507' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 222.02,113.116 274.095,143.182' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 222.02,113.116 194.957,113.116' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 194.957,113.116 167.894,113.116' style='fill:none;fill-rule:evenodd;stroke:#7F7F7F;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<path d='M 274.095,83.0507 274.095,143.182' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />\n",
       "<text x='201.992' y='14.3182' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>O</tspan></text>\n",
       "<text x='155.883' y='121.366' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#7F7F7F' ><tspan style='baseline-shift:super;font-size:11.25px;'>2</tspan><tspan>*</tspan></text>\n",
       "<text x='147.662' y='38.6126' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#7F7F7F' ><tspan style='baseline-shift:super;font-size:11.25px;'>3</tspan><tspan>*</tspan></text>\n",
       "</svg>\n"
      ],
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fd494ab0800>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags = Chem.FragmentOnBonds(Chem.MolFromSmiles('CCOC1CC1'),(2,))\n",
    "frags"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'[2*]C1CC1.[3*]OCC'"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.MolToSmiles(frags,True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pieces = Chem.GetMolFrags(frags,asMols=True)\n",
    "len(pieces)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['[3*]OCC', '[2*]C1CC1']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[Chem.MolToSmiles(x,True) for x in pieces]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from rdkit.Chem import AllChem\n",
    "m = Chem.MolFromSmiles('CCOC1CC1')\n",
    "m.SetProp(\"_Name\",\"test molecule\")\n",
    "AllChem.Compute2DCoords(m)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "test molecule\n",
      "     RDKit          2D\n",
      "\n",
      "  6  6  0  0  0  0  0  0  0  0999 V2000\n",
      "   -3.0582   -0.0065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.6205    0.4213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.5311   -0.6098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.9066   -0.1820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.3656   -0.5303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.9377    0.9074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  1  0\n",
      "  3  4  1  0\n",
      "  4  5  1  0\n",
      "  5  6  1  0\n",
      "  6  4  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(Chem.MolToMolBlock(m))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(2, 8)]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# test that for loops work:\n",
    "atns = []\n",
    "for at in m.GetAtoms():\n",
    "    if at.GetAtomicNum()>6:\n",
    "        atns.append((at.GetIdx(),at.GetAtomicNum()))\n",
    "atns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(2, 8)]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "atns = []\n",
    "for at in m.GetAtoms():\n",
    "    if at.GetAtomicNum()>6:\n",
    "        atns.append((at.GetIdx(),at.GetAtomicNum()))\n",
    "atns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "for at in m.GetAtoms():\n",
    "    if at.GetAtomicNum()>6:\n",
    "        atns.append((at.GetIdx(),at.GetAtomicNum()))\n",
    "if(len(atns)==1):        \n",
    "    atns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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